Initial import

4 files changed, 118 insertions, 0 deletions

diff --git a/.AURINFO b/.AURINFO
new file mode 100644
index 000000000000..d6cb4a1c4e21
--- /dev/null
+++ b/.AURINFO
@@ -0,0 +1,17 @@
+pkgbase = repeatmasker
+	pkgdesc = Screen DNA sequences for interspersed repeats and low complexity DNA sequences
+	pkgver = 4.0.5
+	pkgrel = 1
+	url = http://www.repeatmasker.org/
+	install = repeatmasker.install
+	arch = any
+	license = custom
+	depends = perl
+	depends = hmmer
+	depends = rmblast
+	depends = trf
+	depends = perl-text-soundex
+	source = http://www.repeatmasker.org/RepeatMasker-open-4-0-5.tar.gz
+
+pkgname = repeatmasker
+
diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..e85cc40e6aa4
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,18 @@
+pkgbase = repeatmasker
+	pkgdesc = Screen DNA sequences for interspersed repeats and low complexity DNA sequences
+	pkgver = 4.0.5
+	pkgrel = 1
+	url = http://www.repeatmasker.org/
+	install = repeatmasker.install
+	arch = any
+	license = custom
+	depends = perl
+	depends = hmmer
+	depends = rmblast
+	depends = trf
+	depends = perl-text-soundex
+	source = http://www.repeatmasker.org/RepeatMasker-open-4-0-5.tar.gz
+	md5sums = 6dd3a49044ff288f3c7d30f1ce61e418
+
+pkgname = repeatmasker
+
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..f2d4806115fd
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,26 @@
+# Maintainer: Ben Booth <benwbooth@gmail.com>
+pkgname=repeatmasker
+pkgver=4.0.5
+pkgrel=1
+pkgdesc="Screen DNA sequences for interspersed repeats and low complexity DNA sequences"
+arch=('any')
+url="http://www.repeatmasker.org/"
+license=('custom')
+depends=('perl' 'hmmer' 'rmblast' 'trf' 'perl-text-soundex')
+source=('http://www.repeatmasker.org/RepeatMasker-open-4-0-5.tar.gz')
+md5sums=('6dd3a49044ff288f3c7d30f1ce61e418')
+install='repeatmasker.install'
+
+package() {
+  cd "${srcdir}"/RepeatMasker
+  install -d "${pkgdir}"/usr/share/licenses/repeatmasker
+  install -D -m644 license.txt "${pkgdir}"/usr/share/licenses/repeatmasker/LICENSE
+
+  install -d "${pkgdir}"/usr/lib/RepeatMasker
+  find . -type d -exec install -d "${pkgdir}"/usr/lib/RepeatMasker/'{}' \;
+  find . -type f \! -executable -exec install -D -m644 '{}' "${pkgdir}"/usr/lib/RepeatMasker/'{}' \;
+  find . -type f -executable -exec install -D -m755 '{}' "${pkgdir}"/usr/lib/RepeatMasker/'{}' \;
+
+  install -d "${pkgdir}"/usr/bin
+  ln -sf /usr/lib/RepeatMasker/RepeatMasker "${pkgdir}"/usr/bin/RepeatMasker
+}
diff --git a/repeatmasker.install b/repeatmasker.install
new file mode 100644
index 000000000000..a6cd51937d85
--- /dev/null
+++ b/repeatmasker.install
@@ -0,0 +1,57 @@
+# Configure RepeatMasker. The prompts are:
+# PRESS ENTER TO CONTINUE
+# Enter path [ perl ]:
+# REPEATMASKER INSTALLATION DIRECTORY Enter path
+# TRF PROGRAM Enter path
+# 2. RMBlast - NCBI Blast with RepeatMasker extensions: [ Un-configured ]
+# RMBlast (rmblastn) INSTALLATION PATH
+# Do you want RMBlast to be your default search engine for Repeatmasker?
+# 4. HMMER3.1 & DFAM
+# HMMER INSTALLATION PATH Enter path
+# Do you want HMMER to be your default search engine for Repeatmasker?
+# 5. Done
+
+post_install() {
+  set -e
+  cd /usr/lib/RepeatMasker
+
+  cat << 'EOF' > /usr/lib/RepeatMasker/config.txt
+
+/usr/bin/perl
+/usr/lib/RepeatMasker
+/usr/bin/trf
+2
+/usr/bin
+Y
+4
+/usr/bin
+N
+5
+EOF
+
+  perl ./configure </usr/lib/RepeatMasker/config.txt >/dev/null
+
+  cat << 'EOF'
+RepeatMasker is now ready to use.
+The program is installed with a minimal repeat library
+by default.  This library only contains simple, low-complexity,
+and common artefact ( contaminate ) sequences.  These are
+adequate for use with your own custom repeat library.  If you
+plan to search using common species specific repeats you will
+need to obtain the complete RepeatMasker repeat library from
+GIRI ( www.girinst.org ) and install it:
+  cd /usr/lib/RepeatMasker
+  tar zxvf repeatmaskerlibraries-20140131.tar.gz
+  ./configure <config.txt
+
+The default aligner is RMBlast. You may reconfigure RepeatMasker
+by running
+  cd /usr/lib/RepeatMasker && ./configure
+EOF
+
+}
+
+post_upgrade() {
+  post_install $1
+}
+